Quantitative proteomic analysis of auxin signaling during seedling development

Kelley, Dior R.; Shen, Zhouxin; Walley, Justin W.; Chapman, Elisabeth J.; Briggs, Steven P.; Estelle, Mark

doi:10.1101/211532

Cited by 4 publications

(9 citation statements)

References 70 publications

(86 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Auxin‐regulated gene expression has been well‐characterized and influences many aspects of seedling growth and development. We recently quantified auxin‐regulated proteome remodeling in 5‐day‐old Arabidopsis seedlings (Clark et al., 2019; Kelley et al., 2017) and found widespread changes in protein abundance not linked to transcriptional changes. In order to explore and test this idea further, we examined auxin responsive proteins from our dataset to identify putative candidate proteins which could underlie post‐transcriptional auxin‐mediated gene expression.…”

Section: Resultsmentioning

confidence: 99%

“…In order to explore and test this idea further, we examined auxin responsive proteins from our dataset to identify putative candidate proteins which could underlie post‐transcriptional auxin‐mediated gene expression. One top candidate was the protein IMMUNOREGULATORY RNA‐BINDING PROTEIN (IRR; AT3G23900) which increased in abundance in response to auxin (Kelley et al., 2017) and is known to influence mRNA splicing in Arabidopsis (Dressano et al., 2020).…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

slim shady is a novel allele of PHYTOCHROME B present in the T‐DNA line SALK_015201

Dash

McEwan²,

Montes

et al. 2021

Plant Direct

Self Cite

View full text Add to dashboard Cite

Auxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin, rapid changes in transcript and protein abundance occur in hypocotyls, and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin‐regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we called slim shady , in an annotated insertion line in IMMUNOREGULATORY RNA‐BINDING PROTEIN ( IRR ). Overexpression of the IRR gene failed to rescue the slim shady phenotype and characterization of a second T‐DNA allele of IRR found that it had a wild‐type (WT) hypocotyl length. The slim shady mutant has an elevated expression of numerous genes associated with the brassinosteroid‐auxin‐phytochrome (BAP) regulatory module compared to WT, including transcription factors that regulate brassinosteroid, auxin, and phytochrome pathways. Additionally, slim shady seedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence data and genetic complementation analysis with SALK_015201C, we determined that a novel single nucleotide polymorphism in PHYTOCHROME B was responsible for the slim shady phenotype. This is predicted to induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase‐related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses with phyb‐9 confirmed that slim shady is a mutant allele of PHYB . This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin‐dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T‐DNA stocks.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

slim shady is a novel allele of PHYTOCHROME B present in the T‐DNA line SALK_015201

Dash

McEwan²,

Montes

et al. 2021

Plant Direct

Self Cite

View full text Add to dashboard Cite

show abstract

“…Auxin regulated gene expression has been well-characterized and influences many aspects of seedling growth and development. We recently quantified auxin regulated proteome remodeling in five-day-old Arabidopsis seedlings (Clark et al, 2019; Kelley et al, 2017) and found widespread changes in protein abundance not linked to transcriptional changes. In order to explore and test this idea further we examined auxin responsive proteins from our dataset to identify putative candidate proteins which could underlie post-transcriptional auxin-mediated gene expression.…”

Section: Resultsmentioning

confidence: 99%

“…In order to explore and test this idea further we examined auxin responsive proteins from our dataset to identify putative candidate proteins which could underlie post-transcriptional auxin-mediated gene expression. One top candidate was the protein IMMUNOREGULATORY RNA-BINDING PROTEIN (IRR; AT3G23900) which increased in abundance in response to auxin (Kelley et al, 2017) and is known to influence mRNA splicing in Arabidopsis (Dressano et al, 2020).…”

Section: Resultsmentioning

confidence: 99%

“…We recently characterized auxin responsive proteomes (Kelley et al, 2017) and used these data to perform a reverse genetic screen (Page and Grossniklaus, 2002) for seedlings with altered auxin-dependent phenotypes. One of the candidate genes included in this screen was AT3G23900 which has been recently characterized as IRR , a novel RNA-binding protein that is involved in alternatively splicing of its target genes that serve as key defense regulators against pathogen in Arabidopsis (Dressano et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

slim shadyis a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201

Dash

McEwan²,

Montes

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

Auxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin rapid changes in transcript and protein abundance occur in hypocotyls and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin-regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we called slim shady, in an annotated insertion line in IMMUNOREGULATORY RNA-BINDING PROTEIN (IRR). Overexpression of the IRR gene failed to rescue the slim shady phenotype and characterization of a second T-DNA allele of IRR found that it had a wild-type hypocotyl length. The slim shady mutant has an elevated expression of numerous genes associated with the brassinosteroid-auxin-phytochrome (BAP) regulatory module compared to wild-type, including transcription factors that regulate brassinosteroid, auxin and phytochrome pathways. Additionally, slim shady seedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence and transcriptomics data for SALK_015201C we determined that a novel single nucleotide polymorphism in PHYTOCHROME B was responsible for the slim shady phenotype. This is predicted to induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase-related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses with phyb-9 confirmed that slim shady is a mutant allele of PHYB. This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T-DNA stocks.

show abstract

The Class VIII myosin ATM1 is required for root apical meristem function

Olatunji

Clark

Kelley

2022

Preprint

Self Cite

View full text Add to dashboard Cite

Myosins are evolutionarily conserved motor proteins that interact with actin filaments to regulate organelle transport, cytoplasmic streaming and cell growth. Plant-specific Class XI myosin proteins direct cell division and root organogenesis. However, the roles of plant-specific Class VIII myosin proteins in plant growth and development are less understood. Here, we investigated the function of an auxin-regulated Class VIII myosin, Arabidopsis thaliana Myosin 1 (ATM1), using genetics, transcriptomics, and live cell microscopy. ATM1 is expressed in the primary root, adventitious roots and throughout lateral root development. ATM1 is a plasma membrane localized protein that is enriched in actively dividing cells in the root apical meristem (RAM). Loss of ATM1 function results in impaired primary root growth due to decreased RAM size and reduced cell proliferation in a sugar-dependent manner. In ATM1 loss-of-function roots, columella reporter gene expression is diminished, and fewer columella stem cell divisions occur. In addition, atm1-1 roots displayed reduced auxin responses and auxin marker gene expression. Complementation of atm1-1 with a tagged ATM1 driven under the native ATM1 promoter restored root growth and cell cycle progression in the root meristem. Collectively, these results provide novel evidence that ATM1 functions to influence cell proliferation and columella differentiation in primary roots in response to auxin and sugar cues.

show abstract

Quantitative proteomic analysis of auxin signaling during seedling development

Cited by 4 publications

References 70 publications

slim shady is a novel allele of PHYTOCHROME B present in the T‐DNA line SALK_015201

slim shady is a novel allele of PHYTOCHROME B present in the T‐DNA line SALK_015201

slim shadyis a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201

The Class VIII myosin ATM1 is required for root apical meristem function

Contact Info

Product

Resources

About